source: tags/arb_5.1/HELP_SOURCE/oldhelp/arb_edit.hlp

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UP      arb.hlp
UP      glossary.hlp
UP      alignment.hlp
UP      security.hlp
UP      helix.hlp
UP      ecoliref.hlp

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SUB     exportcursor.hlp
SUB     nekey_map.hlp
SUB     submission.hlp
SUB     ne_search.hlp
SUB     ne_replace.hlp
SUB     ne_compl.hlp
SUB     ne_new_sequence.hlp
SUB     ne_copy_sequence.hlp
SUB     ne_align_seq.hlp
SUB     neprops_data.hlp
SUB     neprops.hlp
SUB     helixsym.hlp
SUB     ne_pretty.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********

TITLE           Old Sequence Editor

OCCURRENCE      ARB_NT/Sequence/Other sequence editors/Edit marked sequences (ARB)

DESCRIPTION     The editor allows you to view and modify the sequences of 'marked
                species' (see LINK{glossary.hlp}) and 'SAI' (sequence associated
                information) data stored in the data base, and to insert
                new data. Potential secondary structure is automatically checked
                and the information can be displayed with the primary structure.
                Protection levels can be assigned to the sequences and 'SAI'
                entries individually.

                The editor permanently communicates with the database and
                other ARB tools. Every change made by the editor is immediately
                exported to the database. All sequence changes made by other
                ARB tools are exported to the editor every 5 seconds.

                Multiple editors can be used synchronously.


        Display:

                        The first column of the editing area of the 'ARB_EDIT'
                        window shows the protection levels. The names of
                        sequences (> name<) and SAI entries (# name#) are listed
                        in column 2.
                        @@@ sequences

        Cursor:

                        The cursor can be moved using the mouse or the arrow
                        keys. The current cursor positions with respect to the
                        alignment and the E. coli sequence (there has to be an
                        'SAI' entry: ECOLI) are indicated after the 'abs-pos'
                        and 'ecoli-pos' prompts in the upper part of the
                        'ARB_EDIT' window, respectively.

        Moving entries:

                        To move an individual entry, position the cursor on the
                        name, keep the left mouse button pressed, move the entry
                        to the desired position, and release the button.

                        Any entry can be fixed (keeps its position while
                        scrolling) at the top or bottom of the editing area by
                        moving it beyond this area.

        Editing:


                Protection:

                        To perform editing, the protection level of the
                        particular entry has to be set to 0 (select protection
                        from the 'EDIT' menu of the 'ARB_EDIT' window) or the
                        protection has to be set globally (press the
                        'Protection' button in the upper part of the 'ARB_EDIT'
                        window) to a level equal to or higher than that assigned to
                        the entry.

                Modes:

                        There are three editing modes which can be selected
                        by pressing F1 or the <align/insert/replace> button
                        in the upper part of the 'ARB_EDIT' window.

                        Nucleotide (amino acid) and gap symbols can be assigned
                        to any of the letter and symbol keys by using the 'Key
                        Mapping' facility ('EDIT' menu).

                        Typing can be done in both directions. Select 5'>3' or
                        3'>5' by pressing the <orientation> button.

                        Replace:

                                Any character right (5'>3') or left (3'>5') to
                                the cursor is replaced by nucleotide (aminoacid)
                                and gap symbols. Characters are deleted ('Del'
                                and 'Backspace' keys) right (5'>3') or left
                                (3'>5') of the cursor

                        Insert:

                                Nucleotide (amino acid) and gap symbols are
                                inserted or deleted ('Del' and 'Backspace'
                                keys) right (5'>3') or left (3'>5') of the
                                cursor.

                        Align + Sequence check:

                                Only gap symbols are inserted or deleted ('Del'
                                and 'Backspace' keys) right (5'>3') or left
                                (3'>5') of the cursor.

                                Sequence check is performed by typing nucleotide
                                (aminoacid) symbols. Discrepancies between typed
                                and existing symbols are indicated by beeping.

                                @@@ Zahlen vervielfachen die Eingabe

                Moving nucleotide (amino acid) symbols:

                        CTRL + LEFT/RIGHT

                             Push or pull a coherent sequence
                             stretch next to the cursor.

                        ALT + LEFT/RIGHT

                            Move a single nucleotide (amino acid) symbol from right or
                            left to the cursor position.

                            If the cursor is placed at a gap position adjacent to a nucleotide (amino acid)
                            symbol this symbol is moved in the direction of cursor position to the next
                            symbol (jumps over gaps).

                        @@ Shift left and Right
                        @@ MG Knopf

EXAMPLES        None

NOTES           The order of the entries cannot be saved to the database.
                The cursor is removed if it is scrolled outside the visible
                area.

                You may use the META key instead of ALT (especially if there is no ALT key :)

WARNINGS        The key mappings may conflict with some window managers
                (eg. olvwm). Disable the CTRL-LEFT/RIGHT keys of the window
                manager.

                If you perform major database modifications such as

                        - changing the length of the alignment
                        - adding new SAIs

                you have to QUIT and restart the editor.

                @@@ MG jump

BUGS            Moving the cursor up and down does not scroll the window.